rs2711669

Variant names:

• chr12-59735191-G-A
• rs2711669
• NM_001270623.2:c.217+30173G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001270623.2(SLC16A7):​c.217+30173G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.123 in 152,070 control chromosomes in the GnomAD database, including 1,500 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.12 (1500 hom., cov: 33)
• Consequence: SLC16A7 NM_001270623.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.232
• Publications: 3 publications found

Genes affected

SLC16A7 (HGNC:10928): (solute carrier family 16 member 7) This gene is a member of the monocarboxylate transporter family. Members in this family transport metabolites, such as lactate, pyruvate, and ketone bodies. The protein encoded by this gene catalyzes the proton-linked transport of monocarboxylates and has the highest affinity for pyruvate. This protein has been reported to be more highly expressed in prostate and colorectal cancer specimens when compared to control specimens. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2012]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.217 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC16A7	NM_001270623.2	c.217+30173G>A		intron_variant	Intron 3 of 5	ENST00000547379.6	NP_001257552.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC16A7	ENST00000547379.6	c.217+30173G>A		intron_variant	Intron 3 of 5	1	NM_001270623.2	ENSP00000448071.1

Frequencies

GnomAD3 genomes AF: 0.123 AC: 18658 AN: 151952 Hom.: 1496 Cov.: 33

Gnomad AFR AF: 0.221

Gnomad AMI AF: 0.0626

Gnomad AMR AF: 0.0797

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.0270

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.0528

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.0869

Gnomad OTH AF: 0.115

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.123 AC: 18672 AN: 152070 Hom.: 1500 Cov.: 33 AF XY: 0.122 AC XY: 9039 AN XY: 74348

African (AFR) AF: 0.221 AC: 9171 AN: 41462

American (AMR) AF: 0.0795 AC: 1216 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.150 AC: 518 AN: 3464

East Asian (EAS) AF: 0.0267 AC: 138 AN: 5174

South Asian (SAS) AF: 0.168 AC: 810 AN: 4822

European-Finnish (FIN) AF: 0.0528 AC: 559 AN: 10580

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.0869 AC: 5907 AN: 67970

Other (OTH) AF: 0.115 AC: 242 AN: 2108

Alfa AF: 0.110 Hom.: 214

Bravo AF: 0.124

Asia WGS AF: 0.109 AC: 379 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.3
DANN	Benign	0.70
PhyloP100		0.23
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2711669; hg19: chr12-60128972;